Zinc in PDB 8wfo: Durio Zibethinus Trypsin Inhibitor Dzti-4

The structure of Durio Zibethinus Trypsin Inhibitor Dzti-4, PDB code: 8wfo was solved by P.Deentanya, K.Wangkanont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.65 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.5, 64.281, 128.404, 90, 90, 90
R / Rfree (%)	17.6 / 20.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Durio Zibethinus Trypsin Inhibitor Dzti-4 (pdb code 8wfo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Durio Zibethinus Trypsin Inhibitor Dzti-4, PDB code: 8wfo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:59.2 occ:0.47 O A:HOH599 2.4 43.7 1.0 OD1 A:ASP139 2.5 21.9 1.0 O A:HOH525 2.9 36.2 1.0 CG A:ASP139 3.4 25.3 1.0 OD2 A:ASP139 3.4 26.6 1.0 O A:HOH598 3.5 46.8 1.0 CA A:THR118 4.4 20.4 1.0 N A:SER119 4.4 18.2 1.0 O A:HOH521 4.6 42.8 1.0 CG2 A:THR118 4.6 18.8 1.0 CB A:ASP139 4.8 15.6 1.0 CB A:THR118 4.8 18.1 1.0 C A:THR118 4.9 22.9 1.0 O A:ASP139 4.9 19.1 1.0

Zinc binding site 2 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:40.5 occ:0.38 O B:HOH640 2.3 31.6 1.0 O A:HOH401 3.1 35.1 1.0 O A:HOH529 3.2 37.6 1.0 O A:HOH500 3.6 42.1 1.0 NZ A:LYS123 3.9 28.9 0.5 O A:HOH478 4.1 17.7 1.0 OD2 A:ASP126 4.1 29.6 1.0 O A:HOH560 4.1 30.4 1.0 NZ A:LYS123 4.3 24.9 0.5 CG A:ASP126 4.9 19.8 1.0 OD1 A:ASP126 5.0 16.9 1.0

Zinc binding site 3 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:18.3 occ:0.35 O A:HOH573 2.0 29.6 1.0 O A:HOH418 2.0 34.1 1.0 OD1 A:ASP125 2.1 19.4 1.0 O A:HOH605 2.1 44.8 1.0 O A:HOH529 2.2 37.6 1.0 CG A:ASP125 3.1 19.3 1.0 OD2 A:ASP125 3.4 25.1 1.0 O A:HOH613 3.6 43.8 1.0 O A:HOH501 4.1 28.3 1.0 O A:HOH424 4.3 24.0 1.0 OD2 A:ASP126 4.3 29.6 1.0 CB A:ASP125 4.4 15.2 1.0 N A:ASP126 4.4 14.7 1.0 O A:HOH495 4.7 31.9 1.0 CA A:ASP125 4.7 13.8 1.0 NZ A:LYS123 4.9 28.9 0.5 CG A:ASP126 4.9 19.8 1.0 CB A:ASP126 4.9 13.8 1.0 O A:HOH560 5.0 30.4 1.0

Zinc binding site 4 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:22.1 occ:0.40 OG A:SER130 2.0 26.2 1.0 O A:HOH545 2.1 43.7 1.0 OD1 A:ASP128 2.1 18.4 1.0 O A:HOH563 2.2 37.0 1.0 O A:HOH546 2.2 32.3 1.0 O A:HOH436 2.6 38.0 1.0 CB A:SER130 2.9 21.8 1.0 CG A:ASP128 3.0 24.2 1.0 OD2 A:ASP128 3.4 20.6 1.0 N A:SER130 3.7 18.3 1.0 CA A:SER130 3.9 22.1 1.0 O A:HOH511 4.3 34.8 1.0 CB A:ASP128 4.4 14.9 1.0 O A:HOH533 4.5 24.5 1.0 O A:HOH585 4.6 36.8 1.0 C A:SER130 4.7 22.1 1.0 CA A:ASP128 4.7 13.6 1.0 C A:ASP128 4.8 16.3 1.0 N A:THR129 4.8 15.1 1.0 O A:HOH592 4.8 46.0 1.0 N A:THR131 4.8 21.1 1.0 C A:THR129 5.0 19.8 1.0

Zinc binding site 5 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:13.3 occ:0.48 OD1 A:ASP37 1.8 19.9 1.0 OE1 A:GLU38 2.0 23.1 1.0 ZN A:ZN307 2.3 32.1 0.4 OE2 A:GLU38 2.4 20.9 1.0 CD A:GLU38 2.5 21.0 1.0 CG A:ASP37 2.9 21.9 1.0 OD2 A:ASP37 3.4 22.1 1.0 N A:GLU38 3.8 15.1 1.0 CG A:GLU38 4.0 19.6 1.0 O A:HOH431 4.1 29.7 1.0 CB A:ASP37 4.1 17.0 1.0 CA A:ASP37 4.2 13.8 1.0 O A:HOH503 4.3 32.8 1.0 NH2 A:ARG40 4.4 20.1 1.0 C A:ASP37 4.5 16.9 1.0 CB A:GLU38 4.6 19.4 1.0 CA A:GLU38 4.8 16.4 1.0 O A:GLU38 4.9 17.3 1.0

Zinc binding site 6 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:32.1 occ:0.42 ZN A:ZN306 2.3 13.3 0.5 O A:HOH431 2.4 29.7 1.0 OE1 A:GLU38 2.8 23.1 1.0 OD1 A:ASP37 3.2 19.9 1.0 O A:HOH503 3.2 32.8 1.0 CD A:GLU38 4.0 21.0 1.0 CG A:ASP37 4.2 21.9 1.0 OE2 A:GLU38 4.4 20.9 1.0 N A:GLU38 4.5 15.1 1.0 CA A:ASP37 4.5 13.8 1.0 O A:GLY36 4.6 21.5 1.0 CB A:ASP37 4.9 17.0 1.0

Zinc binding site 7 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:26.9 occ:0.47 O A:HOH459 2.0 38.1 1.0 O A:HOH566 2.1 45.1 1.0 O A:HOH542 2.2 39.9 1.0 OE1 A:GLU29 2.3 43.8 1.0 CD A:GLU29 3.2 49.4 1.0 OE2 A:GLU29 3.4 55.7 1.0 O A:HOH557 4.3 44.1 1.0 O A:HOH441 4.3 48.1 1.0 CG A:GLU29 4.6 39.8 1.0

Zinc binding site 8 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:21.5 occ:0.42 O A:HOH526 2.1 39.7 1.0 OD1 A:ASN28 2.2 30.6 1.0 CG A:ASN28 3.1 31.2 1.0 ND2 A:ASN28 3.5 28.0 1.0 CB A:ASN28 4.5 28.6 1.0 CA A:ASN28 5.0 30.5 1.0

Zinc binding site 9 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn310 b:43.7 occ:0.39 O A:HOH588 2.2 48.8 1.0 NE2 A:HIS188 2.3 38.1 1.0 O A:HOH511 2.7 34.8 1.0 CD2 A:HIS188 3.2 39.5 1.0 CE1 A:HIS188 3.3 37.6 1.0 OD1 A:ASP189 3.8 40.0 1.0 CG2 A:THR131 4.1 26.6 1.0 CG A:HIS188 4.4 32.2 1.0 ND1 A:HIS188 4.4 37.3 1.0 CG A:ASP189 4.5 40.3 1.0 OD2 A:ASP189 4.5 42.6 1.0 O A:SER130 4.8 27.4 1.0

Zinc binding site 10 out of 18 in the Durio Zibethinus Trypsin Inhibitor Dzti-4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Durio Zibethinus Trypsin Inhibitor Dzti-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn311 b:74.4 occ:0.58 OD2 A:ASP92 2.2 61.8 1.0 O A:HOH593 2.3 53.0 1.0 O A:HOH611 2.4 55.4 1.0 O A:HOH561 2.6 57.1 1.0 CG A:ASP92 3.4 53.5 1.0 NZ A:LYS27 3.9 59.5 1.0 OD1 A:ASP92 4.1 54.0 1.0 CB A:ASP92 4.3 49.6 1.0 CB A:LYS94 4.5 54.2 1.0 N A:ASP95 4.7 41.6 1.0 CB A:ASP95 4.8 45.3 1.0 CE A:LYS27 4.9 48.2 1.0

P.Deentanya, K.Wangkanont. Durio Zibethinus Trypsin Inhibitor Dzti-4 To Be Published.